Glomalin, an arbuscular mycorrhizal protein component of soil, can be used as an indicator of terrigenous-derived carbon. We measured glomalin in sediments using the terrestrial end-member as a reference in four coastal settings: (1) intertidal seagrass meadows distributed over a rainfall gradient, (2) sediments inshore and offshore from the mouth of a river, (3) coastal coral reefs at various distances from the shore, and (4) intertidal wetlands with varying levels of groundwater influence. Across the rainfall gradient, glomalin in seagrass meadow sediments increased at sites with high mean annual rainfall during the wet season (r2 = 0.27; F1,29 = 5.75; p = 0.029). Glomalin decreased in inshore river sediments (terrestrial) to offshore (marine) sediments (r2 = 0.81; F1,17 = 71.7; p ≤ 0.0001). Furthermore, glomalin in reef sediments decreased with distance from the shore. The high intertidal was rich in glomalin where groundwater flowed directly into the wetland compared with those with little groundwater influences. Our data indicate that rivers and groundwater transport terrestrial material, and that mangroves, salt marsh, seagrass meadows, and coral reefs accumulate it, but the connections vary among sites, within sites, and seasonally. Variations in glomalin concentrations are indicative of links between the terrestrial and marine environment that reflect proximity, filtration services, and the level of subsidies that marine ecosystems derive from terrestrial sources. Assessment of glomalin contributes to evaluating terrestrial–marine connectivity, and thus provides knowledge to improve catchment management for the protection of marine ecosystems.